adding debuggins messages
fixing VCF glitches. Don't write AC field. Don't output a variant if we don't have candidate alleles for it. Don't output partial fields if we're not reporting any partial read info
fixed problem when reference allele not included as prior allele
testing commit on new branch
testing commit again
removed code dealing with priors and posterios
now processing one locus at a time
got rid of tab file
working onr eading multiple samples
fixing merge
Merge pull request #2 from tfwillems/master

Yo
Added minimum permutation code
Updated to include debugging. Added minimum permutation functions. Changed countkmers to use minimum permutation instead of canonical string.
comitting so ic an switch brnaches. THIS COMMTI DOES NOT COMPILE
committing before removing partial alignment stuff
got rid of partial alignment
removed partial, fixing string out of range problems
multi-sample calling is working
Added -O3 option to makefile for extensive compiler optimization
multi sample calling